Utilities

Utilities for Bio2BEL.

bio2bel.utils.get_data_dir(module_name)

Ensure the appropriate Bio2BEL data directory exists for the given module, then returns the file path.

Parameters

module_name (str) – The name of the module. Ex: ‘chembl’

Return type

str

Returns

The module’s data directory

bio2bel.utils.prefix_directory_join(prefix, *parts)

Join the parts onto the prefix directory.

Return type

str

bio2bel.utils.ensure_path(prefix, url, *, path=None, use_requests=False, force=False, bucket=None, s3_client=None)

Download a file if it doesn’t exist.

Parameters

force (bool) – If set to true, will re-download from source and re-upload to S3

Return type

str

bio2bel.utils.get_connection(connection=None)

Return the SQLAlchemy connection string if it is set.

Order of operations:

1. Return the connection if given as a parameter

2. Check the environment for BIO2BEL_{module_name}_CONNECTION

3. Look in the bio2bel config file for module-specific connection. Create if doesn’t exist. Check the module-specific section for connection

4. Look in the bio2bel module folder for a config file. Don’t create if doesn’t exist. Check the default section for connection

5. Check the environment for BIO2BEL_CONNECTION

6. Check the bio2bel config file for default

7. Fall back to standard default cache connection

Parameters

connection (Optional[str]) – get the SQLAlchemy connection string

Return type

str

Returns

The SQLAlchemy connection string based on the configuration

bio2bel.utils.get_bio2bel_modules()

Get all Bio2BEL modules.

Return type

Mapping[str, module]

bio2bel.utils.clear_cache(module_name, keep_database=True)

Clear all downloaded files.

Return type

None